2024-02-28 REL RCSB RCSB RCSB 2022-09-21 2023-10-04 2023-10-04 2024-02-28 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM071574 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) T32GM007388 United States CryoEM structure of the Dsl1 complex bound to SNAREs Sec20 and Use1 DAmico KA Jeffrey PD Hughson FM Tether, SNARE, Complex, TRANSPORT PROTEIN DAmico KA Stanton AE Shirkey JD Travis SM Jeffrey PD Hughson FM Structure of a membrane tethering complex incorporating multiple SNAREs. Nat.Struct.Mol.Biol. US 31 246 254 2024 38196032 doi:10.1038/s41594-023-01164-8 1545-9985 EMD-28774 consensus EM volume
Consensus map pre-local refinement
 EMD-28760 focused EM volume
Local refinement of Dsl1:Sec39
 EMD-28762 focused EM volume
Local refinement of Dsl1:Tip20
 EMD-28768 focused EM volume
Local refinement of Sec39:Use1:Sec20:Tip20
 EMD-29447 focused EM volume
Local refinement of Sec39:Use1:Sec20:Tip20 #2
 8eki FULLOVERLAP Dsl1 complex bound to SNARE proteins Sec20 and Use1 Dsl1 complex bound to SNARE proteins Sec20 and Use1 0 1 2 3 4 5 Saccharomyces cerevisiae ATCC 204508/S288c 0.25541261 Dsl1 Complex 1 3 4 5 Saccharomyces cerevisiae ATCC 204508/S288c Protein transport protein SEC20 Saccharomyces cerevisiae S288C ATCC 204508 / S288c 0.032244254 1 Escherichia coli BL21 LEVO MVVTFLQDLEVLQDALLNNLQKLSAISRRKESGESKHDNKDSFAAIANEHNDEEEEIEFEDLVNIIESKVSDFESVLKCS IVEMTYKYPELKLQWEKSPRYDQCDKLHIVKLDKQMNEDIYAQLVEELDFVLQFVDWFYCYRLKVKEILRQHHKRDLAWN DEKRDRAIKFHAVDYDKLHQGTSSSSSLTSTSMEKASTREKLLSKTKQLTNNLVRGNQILQSGILQSDLNLDELRAQTNS LTQIDDKYTQFETVFKKTADLVKVLENASHQEKRD P28791 Protein transport protein USE1 Saccharomyces cerevisiae S288C ATCC 204508 / S288c 0.024254781 1 Escherichia coli BL21 LEVO MAETSNDPFLSYVLSSKQLTNLNRLRRKAVTKQLGSSDDNKVSEEFLRYQHTYQREAFEYLQTKHDAHKIMESQYEQYQS SSKTRRYSIDLDSVDAVDTESQTEYPNEEFIDRNEDSEAVMELRKRLLGKGQNKGLGYETTKSVDRQIEDQDTLQQDLIQ DMSKLVGSLKQGAVAFQSALDEDKQVLGAAEIGIQVASQGLMDVSGKLRKYD P53146 Protein transport protein TIP20 Saccharomyces cerevisiae S288C ATCC 204508 / S288c 0.081253062 1 Escherichia coli BL21 LEVO MNGIDDLLNINDRIKQVQNERNELASKLQNLKQSLASNDTEVALSEVIAQDIIEVGASVEGLEQLRAKYGDLQILNKLEK VAVQQTQMQAGVDKLDSFERQLDELAEQPPDQFTLDDVKALHSKLTSVFATVPQINNIDSQYAAYNKLKSKVTGKYNDVI IQRLATNWSNTFDQKLLEAQWDTQKFASTSVGLVKCLRENSTKLYQLSLLYLPLEEETQNGDSERPLSRSNNNQEPVLWN FKSLANNFNVRFTYHFHATSSSSKIETYFQFLNDYLAENLYKCINIFHDDCNGLTKPVIHEQFINYVLQPIRDKVRSTLF QNDLKTLIVLISQILATDKNLLNSFHYHGLGLVSLISDEVWEKWINYEVEMANRQFINITKNPEDFPKSSQNFVKLINKI YDYLEPFYDLDFDLLVRYKLMTCSLIFMNLTSSYLDYILTVDSLNETRTKEQELYQTMAKLQHVNFVYRKIKSLSSNFIF IQLTDIVNSTESKKYNSLFQNVENDYEKAMSTDMQNSIVHRIQKLLKETLRNYFKISTWSTLEMSVDENIGPSSVPSAEL VNSINVLRRLINKLDSMDIPLAISLKVKNELLNVIVNYFTESILKLNKFNQNGLNQFLHDFKSLSSILSLPSHATNYKCM SLHELVKILKLKYDPNNQQFLNPEYIKTGNFTSLKEAYSIKYLKDTKIQDALYRIIYGNIL P33891 Protein transport protein SEC39 Saccharomyces cerevisiae S288C ATCC 204508 / S288c 0.082483797 1 Escherichia coli BL21 LEVO MLEEQLYLLACIFASRADTRNIKKLSTRLGSQSKYLEILCVLWPELDDPKNLLFLRELEEEVQSPEGEETTDEDVIVELL ESDSSLIPLIESDTTTRSNRYHELQEFISKKLNNKTLENFEEWLRERILICNEMIPETPLLYSVLWETAKSKVLSTKFIG WVEGVLKPLDHLNKRLHLIFKINEWEKMPDSELFKIIFDGVEDMQGYIGIADVIEDELAPTLSYGKKWETFITEFFNKQQ FSLKSDTNYQLFIKLYYSLEKGVKDNSEASRKLQSNVVDILFHNSENLFNLSSLTHKLDELWSILSGFPDEITIEEQKTI TALEMKQFMEFFIKCSTKFSFKEIFAITQEEESAQLAHFSSLCHEEFNKANEISSFLQAMYETVLDISKDDKIFTRISMD EKLYSILEILLQMNEFAYIEAIIERFDYSNNTQIYELLVKFFWHFFNNASNGLRKEPEMKKASQTLQIIQKHMSQRAGTN LTKLEVLLEISDKLSHYSINLNKSHNGARDTAFKPSNILEYRDCPLDIISNLLELNPRLYKDLPTTKSLLFGIYDSLSIN REGQTGKVEVDLMVLHIDYALVNLDFGTAYELGKQVFEICQEAGQHMMKALGDEHWLTFYQMGKFVDPNWVDNEIPTEII VLQMSILGRLLEVCPLEEVEIVTSQWSTLELELSARDLVKDKYALDGQNDNKSKVGGIAREIFHNVTNF Q12745 Protein transport protein DSL1 Saccharomyces cerevisiae S288C ATCC 204508 / S288c 0.091445133 1 Escherichia coli BL21 LEVO MKHHHHHHHGAAGTSLYKKAGENLYFQGSMESLFPNKGEIIRELLKDPLILKNDSKRSNGSELELDSSDLLQREAILANE LNILDNLKTFLNLIKEVKTNLNILELENCYYSLQSLRKKMRNNAAYLKQSFNFQQSISTYVDTLHLELVSTLYKILTNGF WKITENSIQFTPTVEWGKDKVHIEYDTFMDFVAQQYFPKGSLDNQAWFILDMTSADSQEQVRAKLNTIMKEYMNLSRIVS MIKNSIFISGKEISYENEKNILVFSKSSSHGQHCVSTVLTSFEAVCDFMLDGLAFRDRKTLSYELGPLFNTEFTKFVKNN ASIILESLDSPLKNLVSVINNKLTRLVAKSEVTNWTHSGKEIQDLLMNKQLYYNLLLDKVLESHISEIRSIFEDPKKSWQ NLEVVELTTSNTNTMSEKIGKNDSDVQNEKELHNAVSKDDDWNWEVEDDDADAWGDEIDVNIDDEEEKTNQEKEKEPEEE ENAWDEAWAIDENIDDASLENGKEHLKAHDVGSLDKDHIEVTQLPKLFLAISQNFKSSFADSHVDEQYFAYKYNLLQTSY MAMCTANFSHNWCQLYVDMRYLIERDEKLYRIKELTRNLLETKLNMKYRIVCQLIRHQLTEFRENERNPSWDATIEKLLP YILKEIVRPLQKIRGEEGSRYLLSFLNFLYNDCVTKEILKWQIISEVNSENLGELVSLLVNNTDIQLLAKEPSYKKMREK FATMGKFLPLHLKEIMEMFYNGDFYLFATDELIQWIELLFADTPLRRNAIDDIYEIRGTALDD P53847 singleParticle particle 3 7.5 150.0 NaCl Sodium Chloride 20.0 C8H18N2O4S HEPES 1.0 C4H10O2S2 DTT 0.05 H(C2H4O)nO(C6H4)C9H19 NP40
Buffer was made fresh from concentrated components and sterile filtered. NP40 was not present during protein purification but was an additive during the grid preparation.
 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY 10.0 ETHANE 100 277.15 FEI VITROBOT MARK IV
Force=0 Wait Time=0 Blot Time=6s Drain Time=0.
Sample was consistently in the thickest regions of ice only, often close to the edges of the carbon hole
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.25 2.5 GATAN K2 SUMMIT (4k x 4k) 1 5857 45.0 1 469193
Particles were template-picked utilizing a low-resolution density map of the complex, generated from an initial subset of the data.
EM density was built without a reference model, and was generated only from refining classes of selected particles
 1 C1 4.5 FSC 0.143 CUT-OFF Coot 0.8.9.1 49947 MAXIMUM LIKELIHOOD cryoSPARC 4.1.1 MAXIMUM LIKELIHOOD cryoSPARC 4.1.1 4 13070.0 cryoSPARC 4.1.1 emd_28204.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 445.59998 445.59998 445.59998 90.0 90.0 90.0 X Y Z -0.08617353 1.3723472 0.0077837794 0.021243798 1.114 1.114 1.114 0.186 AUTHOR Half map B emd_28204_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 -1 -1 -1 400 400 400 445.59998 445.59998 445.59998 90.0 90.0 90.0 X Y Z -0.070665926 0.76394796 0.045833386 0.043729924 1.114 1.114 1.114 AUTHOR Half map A emd_28204_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 -1 -1 -1 400 400 400 445.59998 445.59998 445.59998 90.0 90.0 90.0 X Y Z -0.1001744 0.67942154 0.044286855 0.04234818 1.114 1.114 1.114 AUTHOR Half map A